BioPhysics Atom Class file

Atom.py

import math

class Atom:
    def __init__(self,line):
        
        self.pdb_line=line
        self.number=int(line[6:11])
        self.name=line[12:16].strip()
        
        self.residue_name=line[17:20].strip()
        self.residue_number=int(line[22:26])
        self.chain=line[21]
        self.pdb_line=line
        
        self.x_coordinate=float(line[30:38])
        self.y_coordinate=float(line[38:46])
        self.z_coordinate=float(line[46:54])
        self.coordinates=[self.x_coordinate,self.y_coordinate,self.z_coordinate]


        self.alternal_location_indicator = line[16]
        self.achar = line[26]
        self.occupancy = float(line[54:60])
        self.temperature_factor = float(line[60:66])
        self.segment_identifier = line[72:76]
        self.element_symbol = line[76:78]
        self.charge_on_atom = line[78:80]

        
        
        if "'" in self.name and len(self.residue_name)<3:
            self.label='Sugar'
        elif "P" in self.name and len(self.residue_name)<3:
            self.label='Phosphate'
        elif len(self.residue_name)<3:
            self.label='Base'
        elif self.name in ['N','CA','C']:
            self.label='Backbone'
        else:
            self.label='Sidechain'
            
        
    def __repr__(self):
        return '{0:4s}{1:>5d}{2:<3s}{3:>4s}{4:>4d}'.format(self.name,self.number,self.chain,self.residue_name,self.residue_number)

    def line_to_file(self):
        newline = '{0:<6s}{1:>5d}  {2:<3s}{3}{4:>3s} {5}{6:>4d}{7}   {8:>8.3f}{9:>8.3f}{10:>8.3f}{11:>6.2f}{12:>6.2f}      {13:<4s}{14:>2s}{15:>2s}\n'.format('ATOM', 
                                                        self.number, self.name, self.alternal_location_indicator, 
                                                        self.residue_name, self.chain, self.residue_number, self.achar,
                                                        self.x_coordinate, self.y_coordinate, self.z_coordinate, 
                                                        self.occupancy, self.temperature_factor, self.segment_identifier, self.element_symbol,
                                                        self.charge_on_atom)
        return newline
    
    def distance(self,other):
        return math.sqrt(pow(self.x_coordinate-other.x_coordinate,2)+
                         pow(self.y_coordinate-other.y_coordinate,2)+
                         pow(self.z_coordinate-other.z_coordinate,2))


def translate_atom(start_idx, end_idx, atom):

    start = atom_array[start_idx]
    end = atom_array[end_idx-1]


    vector.x_coordinate = end.x_coordinate - start.x_coordinate
    vector.y_coordinate = end.y_coordinate - start.y_coordinate
    vector.z_coordinate = end.z_coordinate - start.z_coordinate

    atom.x_coordinate += vector.x_coordinate
    atom.y_coordinate += vector.y_coordinate
    atom.z_coordinate += vector.z_coordinate

    atom.number -= (end_idx - start_idx)

    return atom

def translate_AtomArray(start_idx, end_idx, atom_array):
    for atom in atom_array:
        if atom.number >= end_idx:
            atom = translate_atom(atom_array[start_idx], atom_array[end_idx-1], atom)

    return atom_array






#name=raw_input('Please enter PDB file name:\n')
#chain=raw_input('Please enter CHAIN id:\n')

name='1A2Y.pdb'
outputFileName = 'output.pdb'
target = open(outputFileName, 'w')



atom_start = 2741
atom_end = 2756

source=open(name)


for line in source:
    
    if line.startswith('ATOM'):
        atom = Atom(line)
        if atom.number < atom_start:
            target.write(line)            
        else:
            outline = atom.line_to_file()
            print outline
            target.write(outline)



    

01234567890123456789012345678901234567890123456789012345678901234567890123456789
ATOM 6338 CA TYR A 456 60.059 70.952 -26.972 1.00 23.16 C
ATOM 2 P U R 601 86.329 55.822 -34.357 1.00 69.36 P